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Crystal structure of carbohydrate transporter A0QYB3 from Mycobacterium smegmatis str. MC2 155, target EFI-510969, in complex with xylitol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM DL-XYLITOL), RESERVOIR: 0.1 M IMIDAZOLE-HCL, PH 8.0, 0.2M ZINC ACETATE, 2.5M SODIUM CHLORIDE; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.12 42.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.841 α = 90 b = 63.07 β = 90 c = 73.134 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE MIRRORS 2014-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.4 50 99.7 0.111 16.5 14.6 57826 -3 21.085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 98.5 0.72 4.1 13.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.4 47.76 55931 1794 99.66 0.12524 0.124 0.16294 0.178 RANDOM 18.564
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.53 -0.34 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.24 r_sphericity_free 31.607 r_dihedral_angle_4_deg 24.549 r_sphericity_bonded 21.217 r_dihedral_angle_3_deg 13.257 r_scbond_it 11.857 r_scbond_other 11.854 r_scangle_other 11.089 r_long_range_B_refined 8.848 r_long_range_B_other 8.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.24 r_sphericity_free 31.607 r_dihedral_angle_4_deg 24.549 r_sphericity_bonded 21.217 r_dihedral_angle_3_deg 13.257 r_scbond_it 11.857 r_scbond_other 11.854 r_scangle_other 11.089 r_long_range_B_refined 8.848 r_long_range_B_other 8.847 r_rigid_bond_restr 7.378 r_dihedral_angle_1_deg 6.261 r_mcangle_other 5.026 r_mcangle_it 4.94 r_mcbond_it 4.416 r_mcbond_other 4.159 r_angle_refined_deg 1.959 r_angle_other_deg 1.027 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2313 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 73
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement XDS data reduction SCALA data scaling SHELX phasing